Nexus file
| Filename extensions | usually .nex or .nxs |
|---|---|
| Internet media type | application/octet-stream |
| Magic number | '#NEXUS\n' |
| Developed by | Maddison DR, Swofford DL, Maddison WP |
| Initial release | December 1997 |
| Type of format | bioinformatics |
| Open format? | Yes |
The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.[1] Several popular phylogenetic programs such as PAUP*,[2] MrBayes,[3] Mesquite,[4] MacClade[5] and SplitsTree[6] use this format.
Syntax
[edit]A NEXUS file is made out of a fixed header #NEXUS followed by multiple blocks. Each block starts with BEGIN block_name; and ends with END;. The keywords are case-insensitive. Comments are enclosed inside square brackets [...].[7]
There are a few pre-defined block names for common types of data. Examples include:[7]
- TAXA block
- The TAXA block contains information about taxa.
- DATA block
- The DATA block contains the data matrix (e.g. sequence alignment).
- TREES block
- The TREES block contains phylogenetic trees described using the Newick format, e.g.
((A,B),C);:
The following example uses the three block types above:
#NEXUS
Begin TAXA;
Dimensions ntax=4;
TaxLabels SpaceDog SpaceCat SpaceOrc SpaceElf;
End;
Begin data;
Dimensions nchar=15;
Format datatype=dna missing=? gap=- matchchar=.;
Matrix
[ When a position is a "matchchar", it means that it is the same as the first entry at the same position. ]
SpaceDog atgctagctagctcg
SpaceCat ......??...-.a.
SpaceOrc ...t.......-.g. [ same as atgttagctag-tgg ]
SpaceElf ...t.......-.a.
;
End;
BEGIN TREES;
Tree tree1 = (((SpaceDog,SpaceCat),SpaceOrc,SpaceElf));
END;
See also
[edit]References
[edit]- ^ Maddison DR, Swofford DL, Maddison WP (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
- ^ PAUP* Archived 2006-09-03 at the Wayback Machine — Phylogenetic Analysis Using Parsimony *and other methods
- ^ MrBayes
- ^ Mesquite: A modular system for evolutionary analysis
- ^ MacClade
- ^ Huson and Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol Biol Evol (2005) 23 (2): 254-267. https://doi.org/10.1093/molbev/msj030
- ^ a b Detailed NEXUS specification
External links
[edit]- NEXUS file format — detailed explanation with many examples
- NEXUS format — a good description of the format and its uses in the field
- Nexus to phyloXML converter
- NeXML
- Nexus to Fasta converter
